22  Research Compendium

Learning Objectives

After completing this tutorial you should be able to

Download the directory for this project here, make sure the directory is unzipped and move it to your bi328 directory. You can open the Rproj for this module either by double clicking on it which will launch Rstudio or by opening Rstudio and then using File > Open Project or by clicking on the Rproject icon in the top right of your program window and selecting Open Project.

There should be a file named 22_research-compendium.qmd in that project directory. Use that file to work through this tutorial - you will hand in your rendered (“knitted”) quarto file as your homework assignment. So, first thing in the YAML header, change the author to your name. You will use this quarto document to record your answers. Remember to use comments to annotate your code; at minimum you should have one comment per code set1 you may of course add as many comments as you need to be able to recall what you did. Similarly, take notes in the document as we discuss discussion/reflection questions but make sure that you go back and clean them up for “public consumption”.

  • 1 You should do this whether you are adding code yourself or using code from our manual, even if it isn’t commented in the manual… especially when the code is already included for you, add comments to describe how the function works/what it does as we introduce it during the participatory coding session so you can refer back to it.

    • 22.1 An organized, reproducible and shareable workflow

    In Chapter 4 of our labmanual you were introduced to Project management and Rmarkdown Basics. We said that the goal of open science and reproducible research is to make scientific methods, data, and results more transparent, available and reproducible. In that section, you were introduced to Rprojects and quarto documents and the structure of our Project Folders for this semester with the reasoning that this structure would allow you to establish a reproducible workflow that is organized, reproducible, and shareable.

    Consider this

    Briefly discuss the advantages of designing a workflow that fulfills the three-fold goal of being organized, reproducible, and shareable.

    Did it!

    [Your answer here]

    22.2 Research Compendium

    Consider this

    Briefly define what a research compendium is including central components/principles to be effective, then assess whether our typical structure of a project folder fulfills these criteria2.

  • 2 A good place to to start would be to look at what subdirectories we typically include, whether that is consistent or if some folders only show up occassionaly and to think through what the function of each folder is and how they contribute to the core principles that comprise a good research compendium

    • Did it!

    [Your answer here]

    Consider this

    For your data science project you will be asked to submit your entire research compendium along with the rendered quarto report. Go ahead and create a research compendium in your bi3249 directory right now if you haven’t already and initialize the subdirectories, Rproject and quarto documents you will need. Use bullet points to list the contents and hierarchy of your research compendium. Then give a brief description of your sete up - write it as if you were sharing your research compendium with a collaborator that needs to know what function each component has and what you underlying design is.

    Did it!

    [Your answer here]